You can also use something like VMD where you load the trajectory then select your atoms, then increment the frames and extract the xyz coordinates of each of your atoms in the selection. You can do that in 5 lines of TCL script (just don't update the select within selection after each frame or else it will reselect a new set of molecules based on the distance criteria, if you're trying to track the same water molecules from beginning to end).
On 2012-06-05 06:02:22AM -0700, rankinb wrote: > I am interested in pulling out the trajectories (x,y,z coordinates) of water > molecules within a certain distance of my solute molecule. I have tried > using g_select, but that will only give me the atom numbers and not the > trajectories. I can create an index file using this command but > unfortunately each time frame is set as a different group. > > Is there a way to get the trajectories at all frames of only the water > molecules within a specified distance of a solute molecule? > > Thank you very much, > Blake > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Trajectories-tp4998094.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
